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DoctorOhh is correct: CC will scan the configured folders. If you have a case where .mobi files in the folder CC is told to use for mobis are not being found by the scan, I would love to hear about it.
Amazon has made the scan/store process more complicated by adding a second book storage location: Android/data/com.amazon.kindle/files or some such. It isn't clear from my reading what the rules are. My tests indicate that books in the existing /kindle folder are still recognized, but others say that the books must be in the new place or the kindle app will ignore them. Another complication is that Amazon will download books to this new place even if it recognizes books in /kindle. I can change CC to permit launching the kindle app if books are in that directory just for completeness, but I hesitate because I am not sure if there will be unintended and undesired consequences.
As regards asking the kindle app to open the book: we have never found a way to do that. The best we have been able to do is what you saw, CC opens the app and then you navigate to the book. That is one reason I never use the kindle app to read. Given how easy it is to add this functionality in Android, Amazon must have specifically decided not to do it, perhaps as a way of maintaining their walled garden.
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